Germs and smarts

I missed this story when it came out in May, but I heard it being discussed on the radio today.

In mice at least, eating a common soil bacteria seems to make them learn faster.  From the Science Daily report:

"Mycobacterium vaccae is a natural soil bacterium which people likely ingest or breath in when they spend time in nature," says Dorothy Matthews of The Sage Colleges in Troy, New York, who conducted the research with her colleague Susan Jenks.

Previous research studies on M. vaccae showed that heat-killed bacteria injected into mice stimulated growth of some neurons in the brain that resulted in increased levels of serotonin and decreased anxiety.

"Since serotonin plays a role in learning we wondered if live M. vaccae could improve learning in mice," says Matthews.

Matthews and Jenks fed live bacteria to mice and assessed their ability to navigate a maze compared to control mice that were not fed the bacteria.

"We found that mice that were fed live M. vaccae navigated the maze twice as fast and with less demonstrated anxiety behaviors as control mice," says Matthews.

In the radio interview today, the researcher said they really have no idea whether the same thing happens in humans.  But all the same, it's an intriguing idea that being too hygienic may not only be bad for allergies, but might make learning slower too.

Add this to the “things I didn’t know were possible”list

Simon Dexter, a consultant at Leeds Teaching Hospitals and Meeta's surgeon, said that although it was a major operation it was possible to live without a stomach.

That’s from a BBC story about a couple of sisters in England who, due to their genetic susceptibility to stomach cancer, had theirs removed as a precaution.  Unpleasant.

Greatest scandal of 20th century revealed

Plastic Bertrand was more plastic that you knew. (Strangely, he's also morphed into Ellen DeGeneres.)

Behaviour modification required?

Last year I bought a cheap blood pressure machine from the pharmacy. I think I was a bit worried about the number of headaches my wife was having at the time, and as we don't often get our blood pressure checked, it seemed a sensible thing to do.

It indicated no big problem for either of us.

But due to a couple of mornings of dizziness on getting out of bed this week, I checked my own blood pressure again, and if this little machine is correct, it's up considerably since last year. But the readings it's giving for my wife are much worse, even first thing in the morning.

She's off to the doctor today to see if their machine agrees.

I should probably see my doctor too. There are several issues I can see that may need correcting in my current lifestyle:

1. Tony Abbott should stop improving his polling.

2. What? I can't spend a decade not bothering to get any particular exercise at all? I shake my fist at you fate. (Perhaps I shouldn't, that just made me dizzy.)

3. It's the evil influence of cheese. But is life with low fat cheese really worth living?

4. Salt. If, like me, your diet has a substantial Asian influence, salt is something that often comes in heavy doses. My impression is that nearly all men in Japan men go on blood pressure tablets from about the age of 42. (Their obligatory after work drinking sessions don't help too.)

5. Why am I cursed with a wife who is a talented baker, but with children who don't care for her cheesecakes, key lime pies (curse you, overly productive lime tree in the back yard), pecan pies, rhubarb cinnamon cakes, chocolate horns, etc? Hence, it becomes my duty to finish these desserts over 4 or 5 nights. (Neither my wife nor I actually consider ourselves to be fans of sugar or lots of cream; in fact if following an Australian recipe she often reduces the sugar by about one third and they still come out fine.) Seriously, I have asked my wife to stop making so many desserts, but she enjoys baking and resists my calls. It's a nightmare.

6. Blogging / the Internet. You mean I might be healthier by getting up and doing something, anything, physical, and going to bed a bit earlier. As well as avoiding irritants like the aggro commenters at Catallaxy? Well I'll be...

7. Lose weight. I'm pretty sure my calorie intake hasn't substantially increased over the last decade, but the kilograms surreptitiously increase anyway. We're not talking huge amounts, but photos catching me with a relaxed stomach now do embarrass me, and I know losing 5 - 6 kilos would put me in the normal BMI weight range. Maybe I should take up watching late night commercial TV for the latest exercise machine that I can pay off over four easy installments. Technology in them has improved over the last 10 years, hasn't it? In fact, the last time I lost weight was from a lingering stomach virus that reduced appetite for a good two or three weeks. Why can't that be an annual event?

8. Vitamin D. Yes, yes I am sure this is it. I get very little sun now. Happily, I see from an article in the New York Times that this is thought to be related to high blood pressure. I should be off to the pharmacy to see if vitamin D supplements will allow me to continue my sedate, sunless, salt, cheese and cheesecake eating lifestyle to continue.

Any other suggestions are welcome. Of course, we can also always hope the blood pressure machine is malfunctioning. That would be the best outcome of all.

Optimism in pigs

Can you ask a pig if his glass is half full?

Quite a charming bit of research here:

In an experiment reminiscent of Pavlov's dogs, the Newcastle team taught the pigs to associate a note on a glockenspiel with a treat -- an apple -- and a dog training 'clicker' with something unpleasant -- in this case rustling a plastic bag.

The next step was to place half the pigs in an enriched environment -- more space, freedom to roam in straw and play with 'pig' toys -- while the other half were placed in a smaller, boring environment- no straw and only one non-interactive toy.

The team then played an ambiguous noise -- a squeak -- and studied how the pigs responded. Dr Douglas said the results were compelling.

"We found that almost without exception, the pigs in the enriched environment were optimistic about what this new noise could mean and approached expecting to get the treat," she said. "In contrast, the pigs in the boring environment were pessimistic about this new strange noise and, fearing it might be the mildly unpleasant plastic bag, did not approach for a treat.

Crabb on those leaks

Annabel Crabb on those Labor leaks looks at the suspects in her own amusing way. I agree with her that the most plausible source seems Rudd. Or, I would add, persons close to Rudd who he would have the ability to call off.

Rudd's only response yesterday was via a statement from a spokesperson.

Would he not be capable of making a media appearance, not to answer questions, but simply to deny in person that he is the source of the leaks, and deny knowledge of the source, and to publicly call on the leaker to desist and get behind the re-election of a Labor government?

In any event, such anonymous leaks may perversely work (to a degree) in Gillard's favour, at least if their content is as ultimately unimportant as yesterday's. Everyone (even Laurie Oakes, I heard somewhere, although I don't know how to track down his articles on line) seems to agree that Gillard's come out fighting approach worked for her yesterday.

Real prediction vindicated

Real Climate has been running hot lately with:

a. a lengthy guest post by "Tamino" reviewing a book on the hockey stick controversy, and explaining in great detail why McIntyre is wrong. In comments, there is a full blown fisking of the Judith Curry's quasi-defence of the book and McIntyre, and she does not come out of it well.

b. a post noting the surprisingly accurate predictions of global warming from the mid 1970's by Wally Broecker, who even coined the term "global warming". The article notes:

To those who even today claim that global warming is not predictable, the anniversary of Broecker’s paper is a reminder that global warming was actually predicted before it became evident in the global temperature records over a decade later (when Jim Hansen in 1988 famously stated that “global warming is here”).

He wasn't the first to predict warming from CO2, though:

Broecker was not the first to predict CO₂-induced warming. In 1965, an expert report to US President Lyndon B. Johnson had warned: “By the year 2000, the increase in carbon dioxide will be close to 25%. This may be sufficient to produce measurable and perhaps marked changes in climate.” And in 1972, a more specific prediction similar to Broecker’s was published by the eminent atmospheric scientist J.S. Sawyer in Nature (for a history in a nutshell, see my newspaper column here).

The innovation of Broecker’s article – apart from introducing the term “global warming” – was in combining estimates of CO₂ warming with natural variability. His main thesis was that a natural climatic cooling

has, over the last three decades, more than compensated for the warming effect produced by the CO₂ [....] The present natural cooling will, however, bottom out during the next decade or so. Once this happens, the CO₂ effect will tend to become a significant factor and by the first decade of the next century we may experience global temperatures warmer than any in the last 1000 years.

The latter turned out to be correct.

For all the skeptics who thought it was only global cooling being considered in the mid 70's, this is well worth reading.

Past ocean acidification considered

Yet another study looking at what happened in a previous big event of volcano driven ocean acidification 120,000,000 years ago. Yes, shell making plankton survived, morphing into smaller sizes, but at the same time the rate of acidification, and the way it changed at depth, is very different to what's happening now:

It took at least 25,000 years for the new acidity levels reached in the surface waters to transfer to deeper waters, according to the research—and the ocean took 75,000 years to reach its peak acidity for that episode, as well as at least 160,000 years to recover. The length of this episode derives "most probably because several CO2 pulses [volcanic eruptions] contributed to ocean acidification," Erba says. Further, she plans to examine other high CO2 events in the geologic record to see "if the same causes—excess CO2, global warming, ocean acidification—trigger similar effects on marine calcifiers at different times."

But the 25,000-year time lag between acidification of the surface waters and deeper waters is mysterious, points out geoscientist Timothy Bralower of The Pennsylvania State University, who was not involved in this study. "In the modern ocean, a similar input of carbon would involve a lag on the order of centuries," he notes. "So something is very different." And the nannoconids begin to disappear even before the fossil record indicates lighter volcanic carbon isotopes—in other words, presumably before the actual acidification.

Here's the crux:

"The current rate of ocean acidification is about a hundred times faster than the most rapid events" in the geologic past, notes marine geologist William Howard of the Antarctic Climate and Ecosystems Cooperative Research Center in Hobart, Tasmania. Plus, the direct impacts of global warming may complicate the picture—just as modern coral suffer from increased bleaching thanks to warmer ocean temperatures as well as the reduced carbonate exoskeleton–building capacity brought on by ocean acidification. Bralower adds: "The big question is whether modern species will be able to adapt to what I expect will be much more rapid pH reduction in coming centuries."

Phytoplankton worry

Green wet stuff continues to make the news. A new study in Nature indicates a large decline in the amount of phytoplankton in the oceans over the last century:

Phytoplankton activity fluctuates widely according to season and location, making long-term monitoring of trends difficult. An earlier study², based on satellite observations of ocean colour, suggested a link between climate variability and ocean productivity, but this was limited to observations from 1997 to 2006. Boris Worm, a marine biologist at Dalhousie University in Halifax, Canada, and his team have now combined satellite-derived observations of phytoplankton with historical shipboard measurements stretching back to the pioneering days of oceanography.

The research reveals an unsettling centennial downwards trend, superimposed on shorter-term variability. The scientists found that the average global phytoplankton concentration in the upper ocean currently declines by around 1% per year. Since 1950 alone, algal biomass decreased by around 40%, probably in response to ocean warming — and the decline has gathered pace in recent years.

"Clearly, 40% is a huge number," says Paul Falkowski, an oceanographer at Rutgers University in New Brunswick, New Jersey. "This implies that the entire ocean system is out of steady state, slowing down.

Something to worry about? Well, yes:

"This is severely disquieting," adds Victor Smetacek, a marine biologist at the Alfred Wegener Institute of Polar and Marine Research in Bremerhaven, Germany. "One must really digest the very magnitude of this decline and its possible implications."

The culprit is believed to be ocean warming:

In most regions tested, the phytoplankton decline seems to be the result of a 0.5–1.0 °C warming of the upper ocean over the past century. The warming leads to enhanced vertical 'stratification' of ocean layers, thus limiting the supply of nutrients from deeper waters to the surface.

But ocean warming does not explain reduced productivity in regions, including the Arctic Ocean, where algal growth is mainly constrained by sunlight. So scientists must try to find out what other drivers, such as changes in wind and ocean circulation, might force the decline, says Falkowski.

No one is pointing the finger at ocean acidification yet, and (from memory) experiments with bubbling CO2 through phytoplankton have had mixed results. But there was this story recently that increased acidification may affect the availability of iron, which phytoplankton need to grow well. (There is more detail on that study at my earlier post.) So, I wonder if acidification over the last century is part of the explanation.

Fiddling with algae

The New York Times reports on a lot of work being done to genetically alter algae to make it better as a potential large scale source of biofuel.  This is being taken very seriously:

“There are probably well over 100 academic efforts to use genetic engineering to optimize biofuel production from algae,” said Matthew C. Posewitz, an assistant professor of chemistry at the Colorado School of Mines, who has written a review of the field. “There’s just intense interest globally.”

Algae are attracting attention because the strains can potentially produce 10 or more times more fuel per acre than the corn used to make ethanol or the soybeans used to make biodiesel. Moreover, algae might be grown on arid land and brackish water, so that fuel production would not compete with food production. And algae are voracious consumers of carbon dioxide, potentially helping to keep some of this greenhouse gas from contributing to global warming.

But some people are a little concerned:

At a meeting this month of President Obama’s new bioethics commission, Allison A. Snow, an ecologist at Ohio State University, testified that a “worst-case hypothetical scenario” would be that algae engineered to be extremely hardy might escape into the environment, displace other species and cause algal overgrowths that deprive waters of oxygen, killing fish.

And I guess I didn’t realise how important the humble green scum really is:

“About 40 percent of the oxygen that you and I are breathing right now comes from the algae in the oceans,” the genetic scientist J. Craig Venter said at a Congressional hearing in May. “We don’t want to mess up that process.”

 

Corals feel the heat (and the weed)

Sea surface temperatures in the Red Sea are routinely very high, I believe, but there are corals there that cope nonetheless.  There’s a convincing sounding study in Science that indicates their tolerance is approaching its limits:

Sea surface temperature (SST) across much of the tropics has increased by 0.4° to 1°C since the mid-1970s. A parallel increase in the frequency and extent of coral bleaching and mortality has fueled concern that climate change poses a major threat to the survival of coral reef ecosystems worldwide. Here we show that steadily rising SSTs, not ocean acidification, are already driving dramatic changes in the growth of an important reef-building coral in the central Red Sea. Three-dimensional computed tomography analyses of the massive coral Diploastrea heliopora reveal that skeletal growth of apparently healthy colonies has declined by 30% since 1998. The same corals responded to a short-lived warm event in 1941/1942, but recovered within 3 years as the ocean cooled. Combining our data with climate model simulations by the Intergovernmental Panel on Climate Change, we predict that should the current warming trend continue, this coral could cease growing altogether by 2070.

In other coral news, it's reported today that seaweed is encroaching on a significant number of reefs in the Great Barrier Reef, but the reason is said to be poor water quality. However,  I think it’s also worth noting that ocean acidification would be likely to increase that problem.

Her weddings must be interesting

As reported in the Geelong Advertiser:

A "witch" told a traffic cop she was above the law because she was "from another world" before dragging him at high speed down a busy street.

"Your laws and penalties don't apply to me. I'm not accepting them, I'm sorry, I must go, thank you," Eilish De Avalon said, before driving off with Sen-Constable Andrew Logan’s arm caught in her driver's side door, the Geelong Advertiser reports.

The officer was left seriously injured in the incident after being dragged nearly 200m.

De Avalon, who also told police she "had a universal name that is not recognised here", pleaded guilty in the Geelong Magistrates’ Court

And what does this local witch from another world do in her spare time?:

De Avalon, 40, a marriage celebrant who is also a self-confessed witch from the Geelong suburb of Highton

Free will, Kant, the New York Times

There’s a pretty good essay in the NYT about how whether it is right to give up on free will as a result of the experiments which show that an outsider who can read a brain state correctly can know a person’s decision before the person knows it.

Kant gets invoked to argue that free will is still there, and that the free will conundrum basically arises from not realising the limits of reason.  (I think that’s a fair summary, anyway.)

All very interesting.

More details please

Phys.org has a short report up about a new proposed method for removing CO2 from the air, but its very short on details and says nothing about cost.

I did some lengthy posts looking at CO2 removal technology over the last couple of years; I'll link to them here when I have time.

The “pox on both their houses” election continues

Tim Colebatch provides does a good summary of why a large number of voters feel very disappointed by all parties this election.

I also see that  Tony Abbott has gone into “dog whistle” mode well and truly on the Julia as a single woman issue.   I can’t see this working for him.  

Dangerous nuts

According to this report, a prominent anti-vaccination group in New South Wales is not only spreading their mis-information via the Web; they are actively pursuing those who have suffered a tragedy:

When their four-week-old baby daughter Dana died from whooping cough Toni and David McCaffery sought love and healing to ease their grief.

Instead, they say they were subjected to a campaign of harassment and abuse at the hands of anti-vaccination campaigners, a group who were yesterday labelled a serious threat to the public's health and safety….

Its investigation was sparked by two complaints, one from Toni and David McCaffery, whose four-week-old daughter Dana died from whooping cough last year.

The couple, from Lennox Head, allege they were subjected to months of harassment and abuse by Ms Dorey and anti-vaccination campaigners, accusing them of lying about the cause of their daughter's death. They received anonymous letters and emails that said whooping cough was not fatal and vaccinations were not needed.

Mrs McCaffery, whose daughter was too young to be vaccinated when she caught whooping cough, said Ms Dorey also tried to get her baby's medical records from the hospital without permission. ''Instead of love and healing in the weeks after Dana's death, we got ugliness … it has been terrible,'' she said.

It doesn’t explain why the parents were in contact with the group in the first place, but still this sounds like an appalling story.

I mentioned this anti-vaccination group late last year after they appeared on the 7.30 Report under a post headed “Immunisation Dills”.  It deserves the upgrade to “Dangerous Nuts”. 

Important advance (we hope)

There’s  a pretty big story out about how Australian based researchers have made some fundamental advances in understanding Alzheimer disease, and have been able to treat it in mice.  (Yes, I know, stories like this about potential new treatments for various diseases in humans come out all the time, but this one does sound distinctly more important, it seems to me.)

Bring on the cure, please.

Weekend update

*  Tried to make a cream and tomato pasta sauce, but using mostly low fat evaporated milk instead of cream.   (Hey, my wife fed me pork belly the previous two nights – there has to be the occasional attempt at low fat cooking while my middle age spread continues its winter growth.)  It didn’t work properly – the milk seemed to separate into solids or something, although the taste wasn’t bad.    More investigation into evaporated milk recipes needed.

*  Oh no!  Robin Hood series 3 ended on Saturday night, leading to tears not by the kids, but from the parents.   (I had actually shed a tear at the end of series 2 as well.)     It really was a quality family show – great production values, good acting,  action every episode, sometimes funny, all violence bloodless, and characters believable enough to upset you when they unexpectedly die.   (It was pretty good at the unexpected death.)   It will be missed.

* The debate between Gillard and Abbott on Sunday night (pretty much a draw I thought, although I was not sitting watching it every minute) has led to another surge in Gillard earlobe Googlers coming to this blog via my  my 2007 post-election night comment about it.  (Over a thousand a day.)   Even Channel 9 has noted that her earlobes, which looked particularly large during the debate,  had evidently become a distraction to many people on Twitter.  There is a facebook page about it (nothing to do with me), which seems also to have been created immediately after the 2007 election.   I’m not sure, but I think my mention might be a day or so earlier than the creation of the Facebook page.  Hence I am waiting for  Annabel Crabb to interview me about being the first blogger (I think) to be silly enough to note it.    

You've seen the photo; now see the video

The BBC has put up video of that remarkable incident of the whale that decided to have an on board tour of a passing yacht. As I can't embed BBC video directly, I'll put the Youtube version of it here. It's worth watching:

This week's hard to understand physics

Another week, another arXiv paper that seems important, if only I could follow it properly.

This one is about how to understand the quantum "delayed choice" experiments, which on one interpretation can be thought to show "backwards time influence".

This, according to the paper, is not the right way to think about collapsing wave functions. The crucial section of the paper seems to be this:

Although the above expressions are all very simple, the result is, upon second thought, very non-trivial. It shows that in general, the relative time ordering of measurements on separated (but possible entangled) particles A and B doesn’t matter at all....

This makes explicit that a measurement on one particle does not at all influence the other one. (I.e. the operator 1 acts trivially.) The only effect a measurement has, is changing probabilities of other measurements into conditional probabilities, as explained just above. More important, these conditional probabilities hold regardless of the moment at which you perform the measurement on the other particle. Whether it occurs later, earlier or at the same time - that doesn’t matter at all. This forces us to abandon the (popular, but incorrect) view on the wave function collapse as an event stretching out along a space-like slice. Even though this view is appealing, it creates a wrong intuition about the physics involved.

I understand the idea that he says is wrong; I don't understand the alternative way of looking at it that he is suggesting.

By the way, whatever happened to John Cramer's "backward causation" experiment? It's taking a long time for any results to come out.